title: Trait-directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus.
abstract: The aim of this study was to characterize the transcriptome of a balanced polymorphism, under the regulation of a single gene, for phosphate fertilizer responsiveness/arsenate tolerance in wild grass Holcus lanatus genotypes screened from the same habitat. De novo transcriptome sequencing, RNAseq (RNA sequencing) and single nucleotide polymorphism (SNP) calling were conducted on RNA extracted from H. lanatus. Roche 454 sequencing data were assembled into c. 22,000 isotigs, and paired-end Illumina reads for phosphorus-starved (P-) and phosphorus-treated (P+) genovars of tolerant (T) and nontolerant (N) phenotypes were mapped to this reference transcriptome. Heatmaps of the gene expression data showed strong clustering of each P+/P- treated genovar, as well as clustering by N/T phenotype. Statistical analysis identified 87 isotigs to be significantly differentially expressed between N and T phenotypes and 258 between P+ and P- treated plants. SNPs and transcript expression that systematically differed between N and T phenotypes had regulatory function, namely proteases, kinases and ribonuclear RNA-binding protein and transposable elements. A single gene for arsenate tolerance led to distinct phenotype transcriptomes and SNP profiles, with large differences in upstream post-translational and post-transcriptional regulatory genes rather than in genes directly involved in P nutrition transport and metabolism per se.
authors.affiliation: Institute for Global Food Security, Queen's University Belfast, David Keir Building, Malone Road, Belfast, BT9 5BN, UK.
authors.forename: Caroline
authors.initials: C
authors.lastname: Meharg
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK.
authors.forename: Bayezid
authors.initials: B
authors.lastname: Khan
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK.
authors.forename: Gareth
authors.initials: G
authors.lastname: Norton
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK.
authors.forename: Claire
authors.initials: C
authors.lastname: Deacon
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, AB24 3UU, UK.
authors.forename: David
authors.initials: D
authors.lastname: Johnson
authors.affiliation: Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany.
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.affiliation: Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany.
authors.forename: Bruno
authors.initials: B
authors.lastname: Huettel
authors.affiliation: Institute for Global Food Security, Queen's University Belfast, David Keir Building, Malone Road, Belfast, BT9 5BN, UK.
authors.forename: Andrew A
authors.initials: AA
authors.lastname: Meharg
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D001149:Arsenates / Q000494:pharmacology*; D001151:Arsenic / Q000494:pharmacology*; D001483:Base Sequence; D015870:Gene Expression; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D005838:Genotype; D031752:Holcus / Q000235:genetics* / Q000378:metabolism; D010641:Phenotype; D010710:Phosphates / Q000378:metabolism; D010758:Phosphorus / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D018749:RNA, Plant; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D001149:Arsenates; D010710:Phosphates; D018749:RNA, Plant; D010758:Phosphorus; D001151:Arsenic; C025657:arsenic acid
keywords: Holcus lanatus; arsente; phosphorus (P); tolerance; transcriptome